DNA methylation profiling of the human major histocompatibility complex: A pilot study for the Human Epigenome Project

The Human Epigenome Project aims to identify, catalogue, and interpret genome-wide DNA methylation phenomena. Occurring naturally on cytosine bases at cytosine-guanine dinucleotides, DNA methylation is intimately involved in diverse biological processes and the aetiology of many diseases. Differentially methylated cytosines give rise to distinct profiles, thought to be specific for gene activity, tissue type, and disease state. The identification of such methylation variable positions will significantly improve our understanding of genome biology and our ability to diagnose disease. Here, we report the results of the pilot study for the Human Epigenome Project entailing the methylation analysis of the human major histocompatibility complex. This study involved the development of an integrated pipeline for high-throughput methylation analysis using bisulphite DNA sequencing, discovery of methylation variable positions, epigenotyping by matrix-assisted laser desorption/ionisation mass spectrometry, and development of an integrated public database available at http://www.epigenome.org. Our analysis of DNA methylation levels within the major histocompatibility complex, including regulatory exonic and intronic regions associated with 90 genes in multiple tissues and individuals, reveals a bimodal distribution of methylation profiles (i.e., the vast majority of the analysed regions were either hypo- or hypermethylated), tissue specificity, inter-individual variation, and correlation with independent gene expression data

Assessing Italians' Preferences for Mountain Beef Production Using a Best-Worst Scaling Approach

The European Union (EU) regulation on mountain food products represents a great opportunity for beef producers in mountain areas, particularly as the quality-certified food has received more attention from European consumers in recent years. However, for a food-quality system-such as the European Commission's mountain labeling scheme-to be effective, the regulation standards must meet consumer expectations. In Italy, there are few studies on consumer preferences regarding beef and none focused on meat produced in mountain areas. To help fill this gap, this study assessed the preferences of Italian citizens for attributes associated with beef produced in mountain areas and contrasted the results with the EU regulation on mountain food products. Furthermore, factors that explain the heterogeneity of Italians' preferences regarding beef production attributes were analyzed. Data were collected online using a consumer panel, and a best-worst scaling method and latent class analysis were used. The results indicate that Italians expect mountain beef to be healthier and produced according to higher animal welfare standards. Such preferences reveal the existence of a gap between what Italians expect and the quality standards of the EU regulation on mountain food products, a situation that may jeopardize the objectives of the European Commission's mountain labeling scheme

Algorithmic Error Mitigation Scheme for Current Quantum Processors

We present a hardware agnostic error mitigation algorithm for near term quantum processors inspired by the classical Lanczos method. This technique can reduce the impact of different sources of noise at the sole cost of an increase in the number of measurements to be performed on the target quantum circuit, without additional experimental overhead. We demonstrate through numerical simulations and experiments on IBM Quantum hardware that the proposed scheme significantly increases the accuracy of cost functions evaluations within the framework of variational quantum algorithms, thus leading to improved ground-state calculations for quantum chemistry and physics problems beyond state-of-the-art results

Pulse variational quantum eigensolver on cross-resonance based hardware

State-of-the-art noisy digital quantum computers can only execute short-depth quantum circuits. Variational algorithms are a promising route to unlock the potential of noisy quantum computers since the depth of the corresponding circuits can be kept well below hardware-imposed limits. Typically, the variational parameters correspond to virtual $R_Z$ gate angles, implemented by phase changes of calibrated pulses. By encoding the variational parameters directly as hardware pulse amplitudes and durations we succeed in further shortening the pulse schedule and overall circuit duration. This decreases the impact of qubit decoherence and gate noise. As a demonstration, we apply our pulse-based variational algorithm to the calculation of the ground state of different hydrogen-based molecules (H$_2$, H$_3$ and H$_4$) using IBM cross-resonance-based hardware. We observe a reduction in schedule duration of up to $5\times$ compared to CNOT-based Ans\"atze, while also reducing the measured energy. In particular, we observe a sizable improvement of the minimal energy configuration of H$_3$ compared to a CNOT-based variational form. Finally, we discuss possible future developments including error mitigation schemes and schedule optimizations, which will enable further improvements of our approach paving the way towards the simulation of larger systems on noisy quantum devices

Halfvortices in flat nanomagnets

We discuss a new type of topological defect in XY systems where the O(2) symmetry is broken in the presence of a boundary. Of particular interest is the appearance of such defects in nanomagnets with a planar geometry. They are manifested as kinks of magnetization along the edge and can be viewed as halfvortices with winding numbers \pm 1/2. We argue that halfvortices play a role equally important to that of ordinary vortices in the statics and dynamics of flat nanomagnets. Domain walls found in experiments and numerical simulations are composite objects containing two or more of these elementary defects. We also discuss a closely related system: the two-dimensional smectic liquid crystal films with planar boundary condition.Comment: 7 pages, 8 figures, To appear as a chapter in Les Houches summer school on Quantum Magnetis

When IPCC graphs can foster or bias understanding: evidence among decision-makers from governmental and non-governmental institutions

To develop effective climate change policy, decision-makers need to have the best possible understanding of the available climate science. The IPCC Assessment Reports therefore aim to lay the foundation for informed political decision-making by providing policy-relevant information. But how successful are IPCC reports at communicating key findings? Although IPCC reports display key information in graphs, the interpretation of such graphs has received little attention. Here we provide an empirical evaluation of IPCC graph comprehension among IPCC target audience (N = 110), (political) decision-makers from climate-related (non-)governmental organizations from 54 countries, and a comparative sample of German junior diplomats, representing future international decision-makers (N = 33). We assess comprehension of current climate change risk visualizations using two IPCC graphs, one that employs principles of intuitive design, and one that violates principles of intuitive design. Results showed that (i) while a minority of IPCC target audience misinterpreted the intuitive graph, (ii) the majority of participants systematically misinterpreted the counter-intuitive graph, drawing the opposite conclusion from what was meant to be conveyed by the graph, despite (iii) having high confidence in the accuracy of their interpretation. Since misinterpretation of IPCC graphs does not allow for optimal use of the scientific information for policy-making, the results emphasize the importance of IPCC graphs that follow the principles of intuitive design

In situ labeling of DNA reveals interindividual variation in nuclear DNA breakdown in hair and may be useful to predict success of forensic genotyping of hair

Hair fibers are formed by keratinocytes of the hair follicle in a process that involves the breakdown of the nucleus including DNA. Accordingly, DNA can be isolated with high yield from the hair bulb which contains living keratinocytes, whereas it is difficult to prepare from the distal portions of hair fibers and from shed hair. Nevertheless, forensic investigations are successful in a fraction of shed hair samples found at crime scenes. Here, we report that interindividual differences in the completeness of DNA removal from hair corneocytes are major determinants of DNA content and success rates of forensic investigations of hair. Distal hair samples were permeabilized with ammonia and incubated with the DNA-specific dye Hoechst 33258 to label DNA in situ. Residual nuclear DNA was visualized under the fluorescence microscope. Hair from some donors did not contain any stainable nuclei, whereas hair of other donors contained a variable number of DNA-positive nuclear remnants. The number of DNA-containing nuclear remnants per millimeter of hair correlated with the amount of DNA that could be extracted and amplified by quantitative PCR. When individual hairs were investigated, only hairs in which DNA could be labeled in situ gave positive results in short tandem repeat typing. This study reveals that the completeness of DNA degradation during cornification of the hair is a polymorphic trait. Furthermore, our results suggest that in situ labeling of DNA in hair may be useful for predicting the probability of success of forensic analysis of nuclear DNA in shed hair

Rationale, design and conduct of a randomised controlled trial evaluating a primary care-based complex intervention to improve the quality of life of heart failure patients: HICMan (Heidelberg Integrated Case Management) : study protocol

Background: Chronic congestive heart failure (CHF) is a complex disease with rising prevalence, compromised quality of life (QoL), unplanned hospital admissions, high mortality and therefore high burden of illness. The delivery of care for these patients has been criticized and new strategies addressing crucial domains of care have been shown to be effective on patients' health outcomes, although these trials were conducted in secondary care or in highly organised Health Maintenance Organisations. It remains unclear whether a comprehensive primary care-based case management for the treating general practitioner (GP) can improve patients' QoL. Methods/Design: HICMan is a randomised controlled trial with patients as the unit of randomisation. Aim is to evaluate a structured, standardized and comprehensive complex intervention for patients with CHF in a 12-months follow-up trial. Patients from intervention group receive specific patient leaflets and documentation booklets as well as regular monitoring and screening by a prior trained practice nurse, who gives feedback to the GP upon urgency. Monitoring and screening address aspects of disease-specific selfmanagement, (non)pharmacological adherence and psychosomatic and geriatric comorbidity. GPs are invited to provide a tailored structured counselling 4 times during the trial and receive an additional feedback on pharmacotherapy relevant to prognosis (data of baseline documentation). Patients from control group receive usual care by their GPs, who were introduced to guidelineoriented management and a tailored health counselling concept. Main outcome measurement for patients' QoL is the scale physical functioning of the SF-36 health questionnaire in a 12-month follow-up. Secondary outcomes are the disease specific QoL measured by the Kansas City Cardiomyopathy questionnaire (KCCQ), depression and anxiety disorders (PHQ-9, GAD-7), adherence (EHFScBS and SANA), quality of care measured by an adapted version of the Patient Chronic Illness Assessment of Care questionnaire (PACIC) and NTproBNP. In addition, comprehensive clinical data are collected about health status, comorbidity, medication and health care utilisation. Discussion: As the targeted patient group is mostly cared for and treated by GPs, a comprehensive primary care-based guideline implementation including somatic, psychosomatic and organisational aspects of the delivery of care (HICMAn) is a promising intervention applying proven strategies for optimal care. Trial registration: Current Controlled Trials ISRCTN30822978

Animal-related factors associated with moderate-to-severe diarrhea in children younger than five years in western Kenya: A matched case-control study

Background Diarrheal disease remains among the leading causes of global mortality in children younger than 5 years. Exposure to domestic animals may be a risk factor for diarrheal disease. The objectives of this study were to identify animal-related exposures associated with cases of moderate-to-severe diarrhea (MSD) in children in rural western Kenya, and to identify the major zoonotic enteric pathogens present in domestic animals residing in the homesteads of case and control children. Methodology/Principal findings We characterized animal-related exposures in a subset of case and control children (n = 73 pairs matched on age, sex and location) with reported animal presence at home enrolled in the Global Enteric Multicenter Study in western Kenya, and analysed these for an association with MSD. We identified potentially zoonotic enteric pathogens in pooled fecal specimens collected from domestic animals resident at children’s homesteads. Variables that were associated with decreased risk of MSD were washing hands after animal contact (matched odds ratio [MOR] = 0.2; 95% CI 0.08–0.7), and presence of adult sheep that were not confined in a pen overnight (MOR = 0.1; 0.02–0.5). Variables that were associated with increased risk of MSD were increasing number of sheep owned (MOR = 1.2; 1.0–1.5), frequent observation of fresh rodent excreta (feces/urine) outside the house (MOR = 7.5; 1.5–37.2), and participation of the child in providing water to chickens (MOR = 3.8; 1.2–12.2). Of 691 pooled specimens collected from 2,174 domestic animals, 159 pools (23%) tested positive for one or more potentially zoonotic enteric pathogens (Campylobacter jejuni, C. coli, non-typhoidal Salmonella, diarrheagenic E. coli, Giardia, Cryptosporidium, or rotavirus). We did not find any association between the presence of particular pathogens in household animals, and MSD in children. Conclusions and significance Public health agencies should continue to promote frequent hand washing, including after animal contact, to reduce the risk of MSD. Future studies should address specific causal relations of MSD with sheep and chicken husbandry practices, and with the presence of rodents

Assurance of Distributed Algorithms and Systems: Runtime Checking of Safety and Liveness

This paper presents a general framework and methods for complete programming and checking of distributed algorithms at a high-level, as in pseudocode languages, but precisely specified and directly executable, as in formal specification languages and practical programming languages, respectively. The checking framework, as well as the writing of distributed algorithms and specification of their safety and liveness properties, use DistAlgo, a high-level language for distributed algorithms. We give a complete executable specification of the checking framework, with a complete example algorithm and example safety and liveness properties.Comment: Small fixes to improve property specifications, including improvements not in the RV 2020 final versio